Waihao farmer Roger Small says the agreement is ''like apartheid''.
After months of meetings to decide how much nitrogen could be emitted from land in the Lower Waitaki-South Coastal Canterbury catchment to meet Environment Canterbury water quality standards, farmers came up with an equation.
Colin Hurst, who led the farmer meetings, said it was not easy to get agreement and he feared it would be impossible.
Mr Small spoke out at the meeting in Waimate where the agreement was approved by the ECan zone committee. He believes farmers producing low nitrogen emissions are disadvantaged by others producing levels well above the desired amount.
Were it not for the responsible farming methods carried out by the low emitters, the high emitters could not continue their practices while the overall catchment stayed within the limits, he said.
Mr Small preferred the Otago Regional Council method, where all landowners were responsible for the nitrogen entering waterways from their property.
If they did not meet the required water quality standard by 2020, they could apply for a non-notified resource consent for five years. If they still did not meet the standard by 2025, they would have to apply for a notified consent and the council would look closely at their operations.
ECan was taking current land uses into account. Dairy farmers were being allowed to emit a lot more nitrogen than others.
''Otago doesn't believe past or future investment should be part of the equation,'' Mr Small said.
Farmers in sensitive Otago areas could leach 15kg of nitrogen a hectare per year.
On very light soils alongside some of the South Canterbury waterways, farmers who run five cows to the hectare would be allowed to leach 78kg a hectare.
Arable farmers on the same soils would be allowed to leach only 27kg to 30kg a hectare.
There were only a few high leachers, but ECan did not seem to consider that their land use was inappropriate, Mr Small said.
''In Otago, the low emitters are not even around the table.
''This system put the high and low emitters against each other.''
ECan should have approached the high emitters first, he said.
''Even the high emitters admitted they could only do two and a-half to three cows a hectare without bringing in feed.''
Mr Small was emitting about 6kg of nitrogen, but wanted the opportunity to intensify his systems if his children wanted to take over the farm in the future. There was not enough leeway for them to do what others were already doing.
''If my kids want to go into vegetables, they're limited, because the dairy farmer next door has got high emissions.''
The Overseer nutrient budgeting tool being used by ECan was ''not up to it'' for any farming type except dairying, Mr Small said.
In Otago, Overseer was only being used in areas with a water quality problem, whereas all Canterbury farmers had to use it.
The ''good management practice'' matrix adopted by ECan would not be defined until June next year.
- by Sally Brooker